Retailers that use Endless Aisles Lite are unable to track the inventory levels from Endless Aisles warehouses. As a result, it is the retailer's complete responsibility to manage inventory levels within Shopify. Here are two options you can follow:
1). The retailer can leave inventory tracking ON, and then manually adjust inventory values as needed.
2). The retailer can turn inventory tracking OFF for any SKUs. This means that the SKU will always appear as in-stock, and there will be no need to manually update inventory.
For more details on how to manage inventory within Shopify, please refer to Shopify's help center here.